HEADER VIRAL PROTEIN/INHIBITOR 20-JUN-13 4LAJ TITLE Crystal structure of HIV-1 YU2 envelope gp120 glycoprotein in complex TITLE 2 with CD4-mimetic miniprotein, M48U1, and llama single-domain, broadly TITLE 3 neutralizing, co-receptor binding site antibody, JM4 COMPND MOL_ID: 2; COMPND 2 MOLECULE: CD4-mimetic miniprotein M48U1; COMPND 3 CHAIN: K, D, G, C; COMPND 4 ENGINEERED: YES; EXPDTA X-RAY DIFFRACTION REMARK 2 RESOLUTION. 2.14 ANGSTORMS DBREF 4LAJ K 1 28 PDB 4LAJ 4LAJ 1 28 MODRES 4LAJ U2X K 23 TYR O-(CYCLOHEXYLMETHYL)-L-TYROSINE SEQRES 1 K 28 MPT ASN LEU HIS PHE CYS GLN LEU ARG CYS LYS SER LEU SEQRES 2 K 28 GLY LEU LEU GLY ARG CYS ALA DPR THR TYR CYS ALA CYS SEQRES 3 K 28 VAL NH2 ATOM 1 CA MPT K 1 -30.307 30.399 1.552 1.00 52.37 ATOM 2 C MPT K 1 -31.295 29.289 1.654 1.00 51.78 ATOM 3 O MPT K 1 -31.418 28.672 2.743 1.00 57.14 ATOM 4 CB MPT K 1 -28.963 30.081 0.990 1.00 50.88 ATOM 5 SG MPT K 1 -28.106 28.686 1.649 1.00 80.60 ATOM 6 N ASN K 2 -32.097 28.453 0.915 1.00 57.45 ATOM 7 CA ASN K 2 -32.320 27.022 1.078 0.50 63.60 ATOM 8 C ASN K 2 -31.026 26.229 0.910 1.00 66.78 ATOM 9 O ASN K 2 -30.512 26.080 -0.199 1.00 63.80 ATOM 10 CB ASN K 2 -33.378 26.538 0.086 0.50 63.73 ATOM 11 CG ASN K 2 -34.710 27.241 0.271 0.50 66.03 ATOM 12 OD1 ASN K 2 -35.129 27.515 1.397 0.50 68.99 ATOM 13 ND2 ASN K 2 -35.378 27.546 -0.835 0.50 64.35 ATOM 14 N LEU K 3 -30.514 25.716 2.025 1.00 67.08 ATOM 15 CA LEU K 3 -29.231 25.023 2.047 1.00 66.44 ATOM 16 C LEU K 3 -29.199 23.784 1.159 1.00 70.36 ATOM 17 O LEU K 3 -28.232 23.569 0.429 1.00 68.32 ATOM 18 CB LEU K 3 -28.875 24.634 3.481 1.00 64.78 ATOM 19 CG LEU K 3 -27.468 24.075 3.693 1.00 64.67 ATOM 20 CD1 LEU K 3 -26.426 25.007 3.100 1.00 59.69 ATOM 21 CD2 LEU K 3 -27.203 23.837 5.171 1.00 66.70 ATOM 22 N HIS K 4 -30.250 22.972 1.223 1.00 71.93 ATOM 23 CA HIS K 4 -30.298 21.732 0.455 1.00 71.95 ATOM 24 C HIS K 4 -30.178 21.978 -1.043 1.00 69.89 ATOM 25 O HIS K 4 -29.405 21.310 -1.731 1.00 68.09 ATOM 26 CB HIS K 4 -31.593 20.971 0.742 1.00 74.92 ATOM 27 CG HIS K 4 -31.750 19.723 -0.073 1.00 84.15 ATOM 28 ND1 HIS K 4 -30.842 18.688 -0.034 1.00 87.44 ATOM 29 CD2 HIS K 4 -32.708 19.351 -0.955 1.00 84.96 ATOM 30 CE1 HIS K 4 -31.236 17.728 -0.853 1.00 87.94 ATOM 31 NE2 HIS K 4 -32.365 18.106 -1.424 1.00 85.66 ATOM 32 N PHE K 5 -30.943 22.942 -1.542 1.00 66.43 ATOM 33 CA PHE K 5 -30.943 23.255 -2.963 1.00 68.98 ATOM 34 C PHE K 5 -29.597 23.879 -3.328 1.00 62.79 ATOM 35 O PHE K 5 -29.093 23.700 -4.439 1.00 62.90 ATOM 36 CB PHE K 5 -32.107 24.185 -3.311 1.00 82.78 ATOM 37 CG PHE K 5 -32.260 24.442 -4.784 1.00 96.62 ATOM 38 CD1 PHE K 5 -32.654 23.416 -5.629 1.00100.22 ATOM 39 CD2 PHE K 5 -32.038 25.701 -5.322 1.00101.24 ATOM 40 CE1 PHE K 5 -32.809 23.630 -6.984 1.00102.23 ATOM 41 CE2 PHE K 5 -32.192 25.924 -6.682 1.00101.85 ATOM 42 CZ PHE K 5 -32.578 24.886 -7.513 1.00103.06 ATOM 43 N CYS K 6 -29.028 24.625 -2.386 1.00 50.91 ATOM 44 CA CYS K 6 -27.724 25.250 -2.578 1.00 50.44 ATOM 45 C CYS K 6 -26.625 24.197 -2.695 1.00 57.28 ATOM 46 O CYS K 6 -25.749 24.286 -3.557 1.00 55.91 ATOM 47 CB CYS K 6 -27.409 26.205 -1.425 1.00 54.03 ATOM 48 SG CYS K 6 -25.730 26.888 -1.461 1.00 73.99 ATOM 49 N GLN K 7 -26.677 23.199 -1.818 1.00 61.01 ATOM 50 CA GLN K 7 -25.681 22.134 -1.800 1.00 60.39 ATOM 51 C GLN K 7 -25.782 21.287 -3.065 1.00 53.66 ATOM 52 O GLN K 7 -24.775 20.805 -3.576 1.00 61.96 ATOM 53 CB GLN K 7 -25.844 21.274 -0.545 1.00 62.81 ATOM 54 CG GLN K 7 -25.493 22.030 0.733 1.00 70.24 ATOM 55 CD GLN K 7 -25.590 21.178 1.985 1.00 77.78 ATOM 56 OE1 GLN K 7 -26.376 20.232 2.053 1.00 80.06 ATOM 57 NE2 GLN K 7 -24.787 21.515 2.989 1.00 79.03 ATOM 58 N LEU K 8 -27.001 21.119 -3.567 1.00 49.66 ATOM 59 CA LEU K 8 -27.224 20.457 -4.848 1.00 54.52 ATOM 60 C LEU K 8 -26.568 21.249 -5.972 1.00 49.84 ATOM 61 O LEU K 8 -25.885 20.688 -6.827 1.00 52.21 ATOM 62 CB LEU K 8 -28.718 20.302 -5.135 1.00 58.22 ATOM 63 CG LEU K 8 -29.360 18.939 -4.895 1.00 64.88 ATOM 64 CD1 LEU K 8 -29.132 18.483 -3.462 1.00 72.40 ATOM 65 CD2 LEU K 8 -30.848 18.984 -5.225 1.00 63.65 ATOM 66 N ARG K 9 -26.792 22.558 -5.963 1.00 51.41 ATOM 67 CA ARG K 9 -26.273 23.443 -6.996 1.00 52.41 ATOM 68 C ARG K 9 -24.751 23.397 -7.042 1.00 54.17 ATOM 69 O ARG K 9 -24.153 23.188 -8.098 1.00 56.68 ATOM 70 CB ARG K 9 -26.739 24.876 -6.734 1.00 53.02 ATOM 71 CG ARG K 9 -28.188 25.148 -7.099 1.00 57.64 ATOM 72 CD ARG K 9 -28.605 26.571 -6.723 1.00 55.47 ATOM 73 NE ARG K 9 -27.712 27.594 -7.265 1.00 57.93 ATOM 74 CZ ARG K 9 -27.586 28.817 -6.758 1.00 62.48 ATOM 75 NH1 ARG K 9 -28.295 29.171 -5.694 1.00 60.86 ATOM 76 NH2 ARG K 9 -26.753 29.689 -7.314 1.00 57.21 ATOM 77 N CYS K 10 -24.133 23.568 -5.880 1.00 50.29 ATOM 78 CA CYS K 10 -22.682 23.592 -5.779 1.00 50.32 ATOM 79 C CYS K 10 -22.070 22.224 -6.056 1.00 52.64 ATOM 80 O CYS K 10 -20.957 22.129 -6.573 1.00 57.04 ATOM 81 CB CYS K 10 -22.268 24.106 -4.401 1.00 49.14 ATOM 82 SG CYS K 10 -22.860 25.791 -4.075 1.00 54.95 ATOM 83 N LYS K 11 -22.793 21.166 -5.698 1.00 52.21 ATOM 84 CA LYS K 11 -22.369 19.806 -6.017 1.00 55.82 ATOM 85 C LYS K 11 -22.161 19.627 -7.518 1.00 56.20 ATOM 86 O LYS K 11 -21.219 18.966 -7.948 1.00 54.49 ATOM 87 CB LYS K 11 -23.390 18.785 -5.509 1.00 54.28 ATOM 88 CG LYS K 11 -22.824 17.387 -5.304 1.00 65.80 ATOM 89 CD LYS K 11 -23.820 16.481 -4.598 1.00 73.80 ATOM 90 CE LYS K 11 -23.759 15.056 -5.134 1.00 87.53 ATOM 91 NZ LYS K 11 -22.367 14.569 -5.340 1.00 94.90 ATOM 92 N SER K 12 -23.040 20.230 -8.310 1.00 60.26 ATOM 93 CA SER K 12 -22.957 20.120 -9.761 1.00 63.41 ATOM 94 C SER K 12 -21.681 20.771 -10.279 1.00 66.56 ATOM 95 O SER K 12 -21.222 20.474 -11.381 1.00 63.46 ATOM 96 CB SER K 12 -24.175 20.770 -10.420 1.00 56.74 ATOM 97 OG SER K 12 -24.070 22.183 -10.381 1.00 52.25 ATOM 98 N LEU K 13 -21.113 21.661 -9.473 1.00 65.62 ATOM 99 CA LEU K 13 -19.876 22.334 -9.837 1.00 62.98 ATOM 100 C LEU K 13 -18.681 21.638 -9.200 1.00 63.34 ATOM 101 O LEU K 13 -17.538 22.055 -9.381 1.00 70.07 ATOM 102 CB LEU K 13 -19.931 23.804 -9.417 1.00 57.78 ATOM 103 CG LEU K 13 -21.103 24.584 -10.016 1.00 54.40 ATOM 104 CD1 LEU K 13 -21.046 26.049 -9.611 1.00 52.34 ATOM 105 CD2 LEU K 13 -21.133 24.439 -11.532 1.00 57.77 ATOM 106 N GLY K 14 -18.948 20.573 -8.453 1.00 62.72 ATOM 107 CA GLY K 14 -17.886 19.839 -7.792 1.00 62.80 ATOM 108 C GLY K 14 -17.470 20.534 -6.514 1.00 64.22 ATOM 109 O GLY K 14 -16.380 20.301 -5.991 1.00 63.22 ATOM 110 N LEU K 15 -18.354 21.388 -6.008 1.00 64.06 ATOM 111 CA LEU K 15 -18.050 22.215 -4.847 1.00 67.34 ATOM 112 C LEU K 15 -19.000 21.940 -3.688 1.00 66.57 ATOM 113 O LEU K 15 -20.098 21.418 -3.880 1.00 66.98 ATOM 114 CB LEU K 15 -18.126 23.699 -5.219 1.00 65.99 ATOM 115 CG LEU K 15 -17.330 24.185 -6.432 1.00 66.93 ATOM 116 CD1 LEU K 15 -17.514 25.682 -6.618 1.00 61.94 ATOM 117 CD2 LEU K 15 -15.859 23.842 -6.280 1.00 69.40 ATOM 118 N LEU K 16 -18.569 22.291 -2.482 1.00 63.99 ATOM 119 CA LEU K 16 -19.463 22.266 -1.338 1.00 66.68 ATOM 120 C LEU K 16 -20.389 23.472 -1.403 1.00 65.77 ATOM 121 O LEU K 16 -20.019 24.519 -1.932 1.00 61.04 ATOM 122 CB LEU K 16 -18.675 22.268 -0.027 1.00 71.02 ATOM 123 CG LEU K 16 -19.479 22.598 1.234 1.00 75.34 ATOM 124 CD1 LEU K 16 -20.382 21.435 1.635 1.00 75.73 ATOM 125 CD2 LEU K 16 -18.560 23.002 2.381 1.00 77.74 ATOM 126 N GLY K 17 -21.592 23.329 -0.860 1.00 65.42 ATOM 127 CA GLY K 17 -22.504 24.451 -0.773 1.00 60.46 ATOM 128 C GLY K 17 -22.744 24.829 0.672 1.00 57.95 ATOM 129 O GLY K 17 -22.992 23.967 1.513 1.00 54.82 ATOM 130 N ARG K 18 -22.686 26.124 0.959 1.00 58.36 ATOM 131 CA ARG K 18 -23.068 26.620 2.269 1.00 58.89 ATOM 132 C ARG K 18 -23.730 27.979 2.130 1.00 57.10 ATOM 133 O ARG K 18 -23.567 28.665 1.123 1.00 60.74 ATOM 134 CB ARG K 18 -21.855 26.709 3.198 1.00 63.83 ATOM 135 CG ARG K 18 -20.848 27.780 2.817 1.00 77.34 ATOM 136 CD ARG K 18 -19.849 28.009 3.945 1.00 91.26 ATOM 137 NE ARG K 18 -18.629 28.663 3.481 1.00100.50 ATOM 138 CZ ARG K 18 -17.416 28.424 3.973 1.00107.10 ATOM 139 NH1 ARG K 18 -17.255 27.534 4.944 1.00111.06 ATOM 140 NH2 ARG K 18 -16.363 29.070 3.489 1.00105.31 ATOM 141 N CYS K 19 -24.477 28.377 3.148 1.00 49.78 ATOM 142 CA CYS K 19 -25.131 29.672 3.108 1.00 53.06 ATOM 143 C CYS K 19 -24.165 30.799 3.425 1.00 55.03 ATOM 144 O CYS K 19 -23.203 30.635 4.174 1.00 61.26 ATOM 145 CB CYS K 19 -26.309 29.718 4.083 1.00 55.99 ATOM 146 SG CYS K 19 -27.676 28.618 3.657 1.00 86.98 ATOM 147 N ALA K 20 -24.312 32.072 2.843 1.00 23.11 ATOM 148 CA ALA K 20 -23.674 33.336 3.171 1.00 21.13 ATOM 149 C ALA K 20 -24.830 34.271 3.480 1.00 19.11 ATOM 150 O ALA K 20 -25.350 34.936 2.593 1.00 21.03 ATOM 151 CB ALA K 20 -22.879 33.846 1.991 1.00 21.22 ATOM 152 N DPR K 21 -25.271 34.280 4.719 1.00 19.45 ATOM 153 CA DPR K 21 -26.514 34.980 5.045 1.00 19.58 ATOM 154 CB DPR K 21 -26.618 34.821 6.565 1.00 21.72 ATOM 155 CG DPR K 21 -25.876 33.586 6.856 1.00 24.95 ATOM 156 CD DPR K 21 -24.767 33.496 5.860 1.00 25.75 ATOM 157 C DPR K 21 -27.672 34.311 4.329 1.00 19.86 ATOM 158 O DPR K 21 -27.876 33.108 4.486 1.00 22.94 ATOM 159 N THR K 22 -28.361 35.077 3.512 1.00 20.34 ATOM 160 CA THR K 22 -29.519 34.588 2.772 1.00 19.04 ATOM 161 C THR K 22 -29.147 34.121 1.362 1.00 21.36 ATOM 162 O THR K 22 -30.019 33.744 0.575 1.00 22.56 ATOM 163 CB THR K 22 -30.561 35.688 2.623 1.00 20.02 ATOM 164 OG1 THR K 22 -29.971 36.778 1.909 1.00 20.69 ATOM 165 CG2 THR K 22 -31.064 36.167 3.993 1.00 20.34 ATOM 166 N U2X K 23 -27.814 34.051 0.959 1.00 46.93 ATOM 167 C U2X K 23 -26.696 32.320 -0.354 1.00 47.80 ATOM 168 O U2X K 23 -26.267 31.821 0.682 1.00 51.57 ATOM 169 CA U2X K 23 -27.308 33.679 -0.327 1.00 46.41 ATOM 170 CB U2X K 23 -26.402 34.694 -0.942 1.00 41.84 ATOM 171 CG U2X K 23 -26.825 36.133 -0.951 1.00 45.34 ATOM 172 CD1 U2X K 23 -27.842 36.557 -1.846 1.00 46.84 ATOM 173 CD2 U2X K 23 -26.201 37.049 -0.110 1.00 45.38 ATOM 174 CE1 U2X K 23 -28.248 37.966 -1.878 1.00 49.25 ATOM 175 CE2 U2X K 23 -26.618 38.512 -0.143 1.00 46.08 ATOM 176 CZ U2X K 23 -27.607 38.917 -1.007 1.00 49.30 ATOM 177 OH U2X K 23 -27.992 40.250 -1.052 1.00 56.68 ATOM 178 C7 U2X K 23 -28.474 40.783 -2.240 1.00 57.59 ATOM 179 C1 U2X K 23 -28.117 44.386 -3.625 1.00 57.34 ATOM 180 C2 U2X K 23 -28.848 43.333 -2.836 1.00 59.15 ATOM 181 C3 U2X K 23 -27.897 42.098 -2.684 1.00 48.85 ATOM 182 C4 U2X K 23 -26.502 42.537 -2.066 1.00 41.47 ATOM 183 C5 U2X K 23 -25.927 43.762 -2.828 1.00 35.77 ATOM 184 C6 U2X K 23 -26.964 44.845 -2.813 1.00 44.48 ATOM 185 N CYS K 24 -26.640 31.721 -1.522 1.00 45.56 ATOM 186 CA CYS K 24 -25.941 30.453 -1.690 1.00 45.90 ATOM 187 C CYS K 24 -24.497 30.693 -2.109 1.00 46.63 ATOM 188 O CYS K 24 -24.233 31.404 -3.077 1.00 52.35 ATOM 189 CB CYS K 24 -26.641 29.574 -2.721 1.00 50.03 ATOM 190 SG CYS K 24 -25.721 28.070 -3.116 1.00 68.89 ATOM 191 N ALA K 25 -23.564 30.101 -1.374 1.00 47.63 ATOM 192 CA ALA K 25 -22.152 30.209 -1.715 1.00 49.97 ATOM 193 C ALA K 25 -21.550 28.829 -1.935 1.00 53.92 ATOM 194 O ALA K 25 -21.783 27.910 -1.151 1.00 55.59 ATOM 195 CB ALA K 25 -21.395 30.951 -0.624 1.00 46.19 ATOM 196 N CYS K 26 -20.791 28.672 -2.999 1.00 50.88 ATOM 197 CA CYS K 26 -20.188 27.386 -3.228 1.00 55.84 ATOM 198 C CYS K 26 -18.701 27.509 -2.939 1.00 61.77 ATOM 199 O CYS K 26 -18.016 28.358 -3.495 1.00 62.75 ATOM 200 CB CYS K 26 -20.532 26.879 -4.631 1.00 53.19 ATOM 201 SG CYS K 26 -22.259 26.313 -4.754 1.00 69.33 ATOM 202 N VAL K 27 -18.223 26.669 -2.031 1.00 43.98 ATOM 203 CA VAL K 27 -16.867 26.754 -1.516 1.00 47.81 ATOM 204 C VAL K 27 -15.980 25.691 -2.137 1.00 49.50 ATOM 205 O VAL K 27 -16.321 24.515 -2.120 1.00 45.87 ATOM 206 CB VAL K 27 -16.843 26.551 0.004 1.00 51.77 ATOM 207 CG1 VAL K 27 -15.425 26.652 0.534 1.00 56.04 ATOM 208 CG2 VAL K 27 -17.752 27.550 0.689 1.00 58.83 ATOM 209 N NH2 K 28 -14.739 25.869 -2.376 1.00 63.13 TER